Re: Re: [Gusdev-gusdev] GI Number

[Ed R. <ed_...@be...>]

What about the PERL objects in Model/ ?  Do we need to modify any of those so they will work with the modified views?

-Ed


> 
> From: "Deborah F. Pinney" <pi...@pc...>
> Date: 2004/09/27 Mon PM 12:28:38 EDT
> To: Angel Pizarro <an...@pc...>
> CC: Ed Robinson <ed_...@be...>, 
>         Jinal Jhaveri <jjh...@vb...>, 
>         gus...@li...
> Subject: Re: [Gusdev-gusdev] GI Number
> 
> Angel is correct. locus_tag is a relatively new (new to the GBParser) 
> qualifier for existing features, including gene which is already mapped 
> to dots.GeneFeature. Therefore, my advise was wrong, it should not be 
> added to the mapping list in the perl module. Adding this field to the 
> view should fix the problem for "gene" features.
> 
> As genbank adds features and qualifiers and since the parser was tailored 
> for genbank records, we are going to encounter this problem again. A 
> compounding problem is that a qualifier is generally not exclusive to a 
> single feature. In this case, locus_id really should be added to many 
> views.
> 
>                                                    -Debbie
> 
> On Mon, 27 Sep 2004, Angel Pizarro wrote:
> 
> > Deborah F. Pinney wrote:
> >
> >> locus_tag is not in the list of features in the GBParser. It will have to 
> >> be added with a table(actually view) destination. Which view is 
> >> appropriate for this feature? What are the attributes (from the Genbank 
> >> feature table) for this feature? I'll gladly add this and you can test it 
> >> or you can add it and test and then commit to cvs.
> >> 
> > Let me clarify. "locus_tag" is not a GenBank feature, it is a feature 
> > attribute of the GenBank "gene" feature. The feature is belongs to is being 
> > mapped to DoTS::GeneFeature. Here is the example from the GB record for this 
> > feature attribute, available here :
> > http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=46229367
> >
> > gene 
> > <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=46229367&itemID=819&view=gbwithparts> 
> > complement(<6844..>9270)
> >                    /locus_tag="cgd7_10"
> >
> >
> > Thomas' suggestion of adding the attribute "locus_tag" to the GeneFeature 
> > view and recompiling the objects will work in this case, but be a problem for 
> > anyone else trying to capture this feature attribute.
> >
> > The GBParser has several known problems, this being one of them. Maybe we 
> > should start up a wiki for it to aid in development and documentation.
> >
> > Angel
> >
> >
> >> It should be added  >line 808, following my %featureNameTableMapping = (
> >> 
> >> If the attributes are correct in the mapped table (match the genbank 
> >> attributes), this should work. If this table is not in the 
> >> %classChildList, it should also be added to the appropriate line also.
> >> 
> >>                                                -Deborah
> >> 
> >> On Mon, 27 Sep 2004, Ed Robinson wrote:
> >> 
> >>> So far, down here, I can tell that it is parsing the files for crypto 
> >>> correctly, but I is giving me the following error:
> >>> 
> >>> 
> >>> ********GEtting loc below6844
> >>> 
> >>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER 
> >>> GUS::Model::DoTS::GeneFeature   ::      locus_tag       ::      cgd7_10
> >>> 
> >>> Mon Sep 27 10:13:09 2004        INVALID QUALIFIER 
> >>> GUS::Model::DoTS::Transcript    ::      locus_tag       ::      cgd7_10
> >>> 
> >>> Do you have any ideas why it is disliking my locus_tags?  I am running 
> >>> this without the commit on, if it is looking for this again in the 
> >>> database.
> >>> 
> >>> Thanks for all the help on this.  I don't want to change anything that 
> >>> is working, just figure out how to use it.
> >>> 
> >>> -Ed
> >>> 
> >>> 
> >>> 
> >>> 
> >>> 
> >>> Ed Robinson
> >>> 255 Deerfield Rd
> >>> Bogart, GA 30622
> >>> (706)425-9181
> >>> http://www.electedrobinson.com
> >>> 
> >>> --Learn more about the face of your neighbor, and less about your own.
> >>>         -Sargent Shriver
> >>> 
> >>> 
> >>> 
> >> 
> >> 
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> >
> 

Ed Robinson
255 Deerfield Rd
Bogart, GA 30622
(706)425-9181
http://www.electedrobinson.com

--Learn more about the face of your neighbor, and less about your own.
         -Sargent Shriver